The steady world-wide increase in the number of severely immunocompromised patients in most hospitals has made the control and prevention of nosocomial systemic fungal infections a critical quality-of-care standard. Early diagnosis and antifungal prophylaxis of these infections are complicated, so avoiding the acquisition of the pathogen in the case of Aspergillus and minimizing the predisposing risk factors in the case of Candida are more effective approaches. The maintenance of good air quality in critical areas in hospitals is mandatory to reduce the incidence of invasive aspergillosis. We review the currently available Center for Disease Control recommendations and report our own experiences in the field. The indications and problems of fungal environmental and patient surveillance are also discussed.